*/\r
package eu.etaxonomy.cdm.persistence.dao.hibernate.taxon;\r
\r
+import java.lang.reflect.Field;\r
import java.util.ArrayList;\r
+import java.util.Collection;\r
+import java.util.Comparator;\r
+import java.util.HashSet;\r
+import java.util.Iterator;\r
import java.util.List;\r
import java.util.Set;\r
+import java.util.SortedSet;\r
+import java.util.TreeSet;\r
import java.util.UUID;\r
\r
import org.apache.log4j.Logger;\r
import org.apache.lucene.analysis.SimpleAnalyzer;\r
import org.apache.lucene.queryParser.ParseException;\r
import org.apache.lucene.queryParser.QueryParser;\r
-import org.apache.lucene.search.Sort;\r
-import org.apache.lucene.search.SortField;\r
import org.hibernate.Criteria;\r
import org.hibernate.FetchMode;\r
import org.hibernate.Hibernate;\r
-import org.hibernate.LazyInitializationException;\r
import org.hibernate.Query;\r
import org.hibernate.criterion.Criterion;\r
import org.hibernate.criterion.Projections;\r
import org.hibernate.criterion.Restrictions;\r
+import org.hibernate.envers.query.AuditEntity;\r
+import org.hibernate.envers.query.AuditQuery;\r
import org.hibernate.search.FullTextSession;\r
import org.hibernate.search.Search;\r
import org.hibernate.search.SearchFactory;\r
import org.springframework.beans.factory.annotation.Qualifier;\r
import org.springframework.dao.DataAccessException;\r
import org.springframework.stereotype.Repository;\r
+import org.springframework.util.ReflectionUtils;\r
\r
import eu.etaxonomy.cdm.model.common.Annotation;\r
+import eu.etaxonomy.cdm.model.common.Extension;\r
import eu.etaxonomy.cdm.model.common.Marker;\r
import eu.etaxonomy.cdm.model.common.OriginalSource;\r
import eu.etaxonomy.cdm.model.common.RelationshipBase;\r
+import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;\r
+import eu.etaxonomy.cdm.model.description.DescriptionElementBase;\r
+import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
+import eu.etaxonomy.cdm.model.location.NamedArea;\r
+import eu.etaxonomy.cdm.model.media.Rights;\r
import eu.etaxonomy.cdm.model.name.Rank;\r
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
import eu.etaxonomy.cdm.model.taxon.Synonym;\r
import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;\r
import eu.etaxonomy.cdm.model.taxon.TaxonBase;\r
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;\r
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;\r
+import eu.etaxonomy.cdm.model.view.AuditEvent;\r
import eu.etaxonomy.cdm.persistence.dao.QueryParseException;\r
-import eu.etaxonomy.cdm.persistence.dao.common.ITitledDao;\r
import eu.etaxonomy.cdm.persistence.dao.hibernate.AlternativeSpellingSuggestionParser;\r
import eu.etaxonomy.cdm.persistence.dao.hibernate.common.IdentifiableDaoBase;\r
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;\r
import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;\r
+import eu.etaxonomy.cdm.persistence.query.MatchMode;\r
+import eu.etaxonomy.cdm.persistence.query.OrderHint;\r
+\r
\r
/**\r
* @author a.mueller\r
public class TaxonDaoHibernateImpl extends IdentifiableDaoBase<TaxonBase> implements ITaxonDao { \r
private AlternativeSpellingSuggestionParser<TaxonBase> alternativeSpellingSuggestionParser;\r
\r
+ @SuppressWarnings("unused")\r
private static final Logger logger = Logger.getLogger(TaxonDaoHibernateImpl.class);\r
+ \r
+ private String defaultField = "name.titleCache";\r
+ private Class<? extends TaxonBase> indexedClasses[]; \r
\r
public TaxonDaoHibernateImpl() {\r
super(TaxonBase.class);\r
+ indexedClasses = new Class[2];\r
+ indexedClasses[0] = Taxon.class;\r
+ indexedClasses[1] = Synonym.class;\r
}\r
\r
@Autowired(required = false) //TODO switched of because it caused problems when starting CdmApplicationController\r
public void setAlternativeSpellingSuggestionParser(AlternativeSpellingSuggestionParser<TaxonBase> alternativeSpellingSuggestionParser) {\r
- this.alternativeSpellingSuggestionParser = alternativeSpellingSuggestionParser;\r
+ this.alternativeSpellingSuggestionParser = alternativeSpellingSuggestionParser; \r
}\r
+ \r
\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getRootTaxa(eu.etaxonomy.cdm.model.reference.ReferenceBase)\r
public List<Taxon> getRootTaxa(ReferenceBase sec) {\r
return getRootTaxa(sec, CdmFetch.FETCH_CHILDTAXA(), true, false);\r
}\r
- \r
-\r
-\r
+ \r
/* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getRootTaxa(eu.etaxonomy.cdm.model.reference.ReferenceBase, eu.etaxonomy.cdm.persistence.fetch.CdmFetch, java.lang.Boolean, java.lang.Boolean)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getRootTaxa(eu.etaxonomy.cdm.model.name.Rank, eu.etaxonomy.cdm.model.reference.ReferenceBase, eu.etaxonomy.cdm.persistence.fetch.CdmFetch, java.lang.Boolean, java.lang.Boolean)\r
*/\r
- public List<Taxon> getRootTaxa(ReferenceBase sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications) {\r
+ public List<Taxon> getRootTaxa(Rank rank, ReferenceBase sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications, List<String> propertyPaths) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.getRootTaxa(Rank rank, ReferenceBase sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications)");\r
if (onlyWithChildren == null){\r
onlyWithChildren = true;\r
}\r
cdmFetch = CdmFetch.NO_FETCH();\r
}\r
\r
-\r
-// String query = "from Taxon root ";\r
-// query += " where root.taxonomicParentCache is NULL ";\r
-// if (sec != null){\r
-// query += " AND root.sec.id = :sec "; \r
-// } \r
-// Query q = getSession().createQuery(query);\r
-// if (sec != null){\r
-// q.setInteger("sec", sec.getId());\r
-// }\r
-\r
-\r
Criteria crit = getSession().createCriteria(Taxon.class);\r
- crit.add(Restrictions.isNull("taxonomicParentCache"));\r
+ \r
+ crit.setFetchMode("name", FetchMode.JOIN);\r
+ crit.createAlias("name", "name");\r
+ \r
+ if (rank != null) {\r
+ crit.add(Restrictions.eq("name.rank", rank));\r
+ }else{\r
+ crit.add(Restrictions.isNull("taxonomicParentCache"));\r
+ }\r
+\r
if (sec != null){\r
crit.add(Restrictions.eq("sec", sec) );\r
}\r
\r
-\r
if (! cdmFetch.includes(CdmFetch.FETCH_CHILDTAXA())){\r
- logger.warn("no child taxa fetch");\r
+ logger.info("Not fetching child taxa");\r
//TODO overwrite LAZY (SELECT) does not work (bug in hibernate?)\r
crit.setFetchMode("relationsToThisTaxon.fromTaxon", FetchMode.LAZY);\r
}\r
\r
List<Taxon> results = new ArrayList<Taxon>();\r
- for(Taxon taxon : (List<Taxon>) crit.list()){\r
+ List<Taxon> taxa = crit.list();\r
+ for(Taxon taxon : taxa){\r
+ \r
+ \r
//childTaxa\r
//TODO create restriction instead\r
+ // (a) not using cache fields\r
+ /*Hibernate.initialize(taxon.getRelationsFromThisTaxon());\r
+ if (onlyWithChildren == false || taxon.getRelationsFromThisTaxon().size() > 0){\r
+ if (withMisapplications == true || ! taxon.isMisappliedName()){\r
+ defaultBeanInitializer.initialize(taxon, propertyPaths);\r
+ results.add(taxon);\r
+ }\r
+ }*/\r
+ // (b) using cache fields\r
if (onlyWithChildren == false || taxon.hasTaxonomicChildren()){\r
if (withMisapplications == true || ! taxon.isMisappliedName()){\r
+ defaultBeanInitializer.initialize(taxon, propertyPaths);\r
results.add(taxon);\r
}\r
}\r
return results;\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getRootTaxa(eu.etaxonomy.cdm.model.reference.ReferenceBase, eu.etaxonomy.cdm.persistence.fetch.CdmFetch, java.lang.Boolean, java.lang.Boolean)\r
+ */\r
+ public List<Taxon> getRootTaxa(ReferenceBase sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications) {\r
+ return getRootTaxa(null, sec, cdmFetch, onlyWithChildren, withMisapplications, null);\r
+ }\r
+ \r
+\r
public List<TaxonBase> getTaxaByName(String queryString, ReferenceBase sec) {\r
\r
return getTaxaByName(queryString, true, sec);\r
}\r
\r
public List<TaxonBase> getTaxaByName(String queryString, Boolean accepted, ReferenceBase sec) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.getTaxaByName(String name, ReferenceBase sec)");\r
\r
- Criteria criteria = null;\r
+ Criteria criteria = null;\r
if (accepted == true) {\r
criteria = getSession().createCriteria(Taxon.class);\r
} else {\r
criteria = getSession().createCriteria(Synonym.class);\r
}\r
-\r
+ \r
criteria.setFetchMode( "name", FetchMode.JOIN );\r
criteria.createAlias("name", "name");\r
-\r
- if (sec != null){\r
- if(sec.getId() == 0){\r
- getSession().save(sec);\r
- }\r
+ \r
+ if (sec != null && sec.getId() != 0) {\r
criteria.add(Restrictions.eq("sec", sec ) );\r
}\r
+\r
if (queryString != null) {\r
criteria.add(Restrictions.ilike("name.nameCache", queryString));\r
}\r
- List<TaxonBase> results = criteria.list();\r
+\r
+ return (List<TaxonBase>)criteria.list();\r
+ }\r
+\r
+ public List<TaxonBase> getTaxaByName(Class<? extends TaxonBase> clazz, String queryString, MatchMode matchMode,\r
+ Integer pageSize, Integer pageNumber) {\r
+ \r
+ return getTaxaByName(clazz, queryString, matchMode, null, null, pageSize, pageNumber, null);\r
+ }\r
+ \r
+ public List<TaxonBase> getTaxaByName(String queryString, MatchMode matchMode, \r
+ Boolean accepted, Integer pageSize, Integer pageNumber) {\r
+ \r
+ if (accepted == true) {\r
+ return getTaxaByName(Taxon.class, queryString, matchMode, pageSize, pageNumber);\r
+ } else {\r
+ return getTaxaByName(Synonym.class, queryString, matchMode, pageSize, pageNumber);\r
+ }\r
+ }\r
+ \r
+ \r
+ public List<TaxonBase> getTaxaByName(Class<? extends TaxonBase> clazz, String queryString, MatchMode matchMode,\r
+ ReferenceBase sec, Set<NamedArea> namedAreas, Integer pageSize, \r
+ Integer pageNumber, List<String> propertyPaths) {\r
+ \r
+ \r
+ boolean doCount = false;\r
+ \r
+ Query query = prepareTaxaByName(clazz, queryString, matchMode, namedAreas, pageSize, pageNumber, doCount);\r
+\r
+ List<TaxonBase> results = query.list();\r
+ \r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
+ \r
return results;\r
+ \r
+ }\r
+\r
+ /**\r
+ * @param clazz\r
+ * @param queryString\r
+ * @param matchMode\r
+ * @param namedAreas\r
+ * @param pageSize\r
+ * @param pageNumber\r
+ * @param doCount\r
+ * @return\r
+ * \r
+ * FIXME implement taxontree restriction & implement test: see {@link TaxonDaoHibernateImplTest#testCountTaxaByName()}\r
+ */\r
+ private Query prepareTaxaByName(Class<? extends TaxonBase> clazz, String queryString, MatchMode matchMode,\r
+ Set<NamedArea> namedAreas, Integer pageSize, Integer pageNumber, boolean doCount) {\r
+ \r
+ \r
+ //TODO ? checkNotInPriorView("TaxonDaoHibernateImpl.countTaxaByName(String queryString, Boolean accepted, ReferenceBase sec)");\r
+\r
+ String hqlQueryString = matchMode.queryStringFrom(queryString);\r
+ \r
+ String matchOperator;\r
+ if (matchMode == MatchMode.EXACT) {\r
+ matchOperator = "=";\r
+ } else {\r
+ matchOperator = "like";\r
+ }\r
+ \r
+ String selectWhat = (doCount ? "count(distinct t)": "distinct t");\r
+ \r
+ String hql = "";\r
+ Set<NamedArea> areasExpanded = new HashSet<NamedArea>();\r
+ if(namedAreas != null && namedAreas.size() > 0){\r
+ // expand areas\r
+ List<NamedArea> childAreas;\r
+ Query areaQuery = getSession().createQuery("select childArea from NamedArea as childArea left join childArea.partOf as parentArea where parentArea = :area");\r
+ expandNamedAreas(namedAreas, areasExpanded, areaQuery);\r
+ \r
+ if(clazz.equals(Taxon.class)){\r
+ hql = "select " + selectWhat + " from Distribution e join e.inDescription d join d.taxon t join t.name n "+\r
+ " where e.area in (:namedAreas) AND n.nameCache " + matchOperator + " :queryString"; \r
+ } else {\r
+ //FIXME implement\r
+ logger.warn("find synonyms by area not jet implemented");\r
+ hql = "select " + selectWhat + " from Distribution e join e.inDescription d join d.taxon t join t.name n "+\r
+ " where e.area in (:namedAreas) AND n.nameCache " + matchOperator + " :queryString"; \r
+ }\r
+ } else {\r
+ hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t" \r
+ + " where t.name.nameCache " + matchOperator + " :queryString";\r
+ }\r
+ \r
+ if(!doCount){\r
+ hql += " order by t.titleCache"; //" order by t.name.nameCache";\r
+ }\r
+ \r
+ Query query = getSession().createQuery(hql);\r
+ \r
+ query.setParameter("queryString", hqlQueryString);\r
+ if(areasExpanded.size() > 0){\r
+ query.setParameterList("namedAreas", areasExpanded);\r
+ }\r
+ \r
+ if(pageSize != null && !doCount) {\r
+ query.setMaxResults(pageSize);\r
+ if(pageNumber != null) {\r
+ query.setFirstResult(pageNumber * pageSize);\r
+ }\r
+ }\r
+ return query;\r
+ }\r
+ \r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countTaxaByName(java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, eu.etaxonomy.cdm.persistence.query.SelectMode, eu.etaxonomy.cdm.model.reference.ReferenceBase, java.util.Set)\r
+ */\r
+ public long countTaxaByName(Class<? extends TaxonBase> clazz, String queryString, MatchMode matchMode,\r
+ ReferenceBase sec, Set<NamedArea> namedAreas) {\r
+ \r
+ boolean doCount = true;\r
+ Query query = prepareTaxaByName(clazz, queryString, matchMode, namedAreas, null, null, doCount);\r
+ Object result = query.uniqueResult();\r
+ return (Long) result;\r
+ \r
+ }\r
+\r
+ /**\r
+ * @param namedAreas\r
+ * @param areasExpanded\r
+ * @param areaQuery\r
+ */\r
+ private void expandNamedAreas(Collection<NamedArea> namedAreas, Set<NamedArea> areasExpanded, Query areaQuery) {\r
+ List<NamedArea> childAreas;\r
+ for(NamedArea a : namedAreas){\r
+ areasExpanded.add(a);\r
+ areaQuery.setParameter("area", a);\r
+ childAreas = areaQuery.list();\r
+ if(childAreas.size() > 0){\r
+ areasExpanded.addAll(childAreas);\r
+ expandNamedAreas(childAreas, areasExpanded, areaQuery);\r
+ }\r
+ }\r
}\r
+ \r
+// /* (non-Javadoc)\r
+// * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countTaxaByName(java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, eu.etaxonomy.cdm.persistence.query.SelectMode)\r
+// */\r
+// public Integer countTaxaByName(String queryString, MatchMode matchMode, SelectMode selectMode) { \r
+// return countTaxaByName(queryString, matchMode, selectMode, null);\r
+// }\r
+\r
+// /* (non-Javadoc)\r
+// * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countTaxaByName(java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, eu.etaxonomy.cdm.persistence.query.SelectMode, eu.etaxonomy.cdm.model.reference.ReferenceBase)\r
+// */\r
+// public Integer countTaxaByName(String queryString, \r
+// MatchMode matchMode, SelectMode selectMode, ReferenceBase sec) {\r
+//\r
+// Long count = countTaxaByName(queryString, matchMode, selectMode, sec, null);\r
+// return count.intValue();\r
+//\r
+// }\r
+ \r
+// public Integer countTaxaByName(String queryString, MatchMode matchMode, Boolean accepted) {\r
+// \r
+// SelectMode selectMode = (accepted ? SelectMode.TAXA : SelectMode.SYNONYMS);\r
+// Long count = countTaxaByName(queryString, matchMode, selectMode, null, null);\r
+// return count.intValue();\r
+// }\r
+ \r
\r
public List<TaxonBase> getAllTaxonBases(Integer pagesize, Integer page) {\r
- Criteria crit = getSession().createCriteria(TaxonBase.class);\r
- List<TaxonBase> results = crit.list();\r
- // TODO add page & pagesize criteria\r
- return results;\r
+ return super.list(pagesize, page);\r
}\r
\r
public List<Synonym> getAllSynonyms(Integer limit, Integer start) {\r
- Criteria crit = getSession().createCriteria(Synonym.class);\r
- List<Synonym> results = crit.list();\r
- return results;\r
+ return super.list(Synonym.class, limit, start);\r
}\r
\r
public List<Taxon> getAllTaxa(Integer limit, Integer start) {\r
- Criteria crit = getSession().createCriteria(Taxon.class);\r
- List<Taxon> results = crit.list();\r
- return results;\r
+ return super.list(Taxon.class, limit, start);\r
}\r
\r
public List<RelationshipBase> getAllRelationships(Integer limit, Integer start) {\r
- Criteria crit = getSession().createCriteria(RelationshipBase.class);\r
- List<RelationshipBase> results = crit.list();\r
- return results;\r
+ AuditEvent auditEvent = getAuditEventFromContext();\r
+ if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {\r
+ Criteria criteria = getSession().createCriteria(RelationshipBase.class);\r
+ return (List<RelationshipBase>)criteria.list();\r
+ } else {\r
+ AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(RelationshipBase.class,auditEvent.getRevisionNumber());\r
+ return (List<RelationshipBase>)query.getResultList();\r
+ }\r
}\r
-\r
+ \r
+ /** Sets the taxonomic parent to null. Does not handle taxonomic relationships. */\r
+// private boolean nullifyTaxonomicParent(Taxon taxon) {\r
+//\r
+// try {\r
+// Method nullifyTaxonomicParent = taxon.getClass().getMethod("nullifyTaxonomicParent");\r
+// nullifyTaxonomicParent.invoke(taxon);\r
+// } catch (NoSuchMethodException ex) {\r
+// logger.error("NoSuchMethod: " + ex.getMessage());\r
+// return false;\r
+// } catch (IllegalArgumentException ex) {\r
+// logger.error("IllegalArgumentException: " + ex.getMessage());\r
+// return false;\r
+// } catch (IllegalAccessException ex) {\r
+// logger.error("IllegalAccessException: " + ex.getMessage());\r
+// return false;\r
+// } catch (InvocationTargetException ex) {\r
+// logger.error("IllegalAccessException: " + ex.getMessage());\r
+// return false;\r
+// }\r
+// return true;\r
+// }\r
+ \r
@Override\r
public UUID delete(TaxonBase taxonBase) throws DataAccessException{\r
- //getSession().update(taxonBase); doesn't work with lazy collections\r
if (taxonBase == null){\r
logger.warn("TaxonBase was 'null'");\r
return null;\r
}\r
- //annotations\r
- try {\r
- Set<Annotation> annotations = taxonBase.getAnnotations();\r
- for (Annotation annotation: annotations){\r
- taxonBase.removeAnnotation(annotation);\r
- }\r
- } catch (LazyInitializationException e) {\r
- logger.warn("LazyInitializationException: " + e);\r
- }\r
- //markers\r
- try {\r
- Set<Marker> markers = taxonBase.getMarkers();\r
- for (Marker marker: markers){\r
- taxonBase.removeMarker(marker);\r
- }\r
- } catch (LazyInitializationException e) {\r
- logger.warn("LazyInitializationException: " + e);\r
- }\r
- //originalSource\r
- try {\r
- Set<OriginalSource> origSources = taxonBase.getSources();\r
- for (OriginalSource source: origSources){\r
- taxonBase.removeSource(source);\r
- }\r
- } catch (LazyInitializationException e) {\r
- logger.warn("LazyInitializationException: " + e);\r
- }\r
- //is Taxon\r
- TaxonNameBase taxonNameBase =taxonBase.getName();\r
- if (taxonNameBase != null){\r
- taxonNameBase.removeTaxonBase(taxonBase);\r
- }\r
- if (taxonBase instanceof Taxon){\r
+ \r
+ // Merge the object in if it is detached\r
+ //\r
+ // I think this is preferable to catching lazy initialization errors \r
+ // as that solution only swallows and hides the exception, but doesn't \r
+ // actually solve it.\r
+ getSession().merge(taxonBase);\r
+ \r
+ for(Iterator<Annotation> iterator = taxonBase.getAnnotations().iterator(); iterator.hasNext();) {\r
+ Annotation annotation = iterator.next();\r
+ annotation.setAnnotatedObj(null);\r
+ iterator.remove();\r
+ getSession().delete(annotation);\r
+ }\r
+ \r
+ for(Iterator<Marker> iterator = taxonBase.getMarkers().iterator(); iterator.hasNext();) {\r
+ Marker marker = iterator.next();\r
+ marker.setMarkedObj(null);\r
+ iterator.remove();\r
+ getSession().delete(marker);\r
+ }\r
+ \r
+ for(Iterator<Extension> iterator = taxonBase.getExtensions().iterator(); iterator.hasNext();) {\r
+ Extension extension = iterator.next();\r
+ extension.setExtendedObj(null);\r
+ iterator.remove();\r
+ getSession().delete(extension);\r
+ }\r
+ \r
+ for(Iterator<OriginalSource> iterator = taxonBase.getSources().iterator(); iterator.hasNext();) {\r
+ OriginalSource source = iterator.next();\r
+ source.setSourcedObj(null);\r
+ iterator.remove();\r
+ getSession().delete(source);\r
+ }\r
+\r
+ for(Iterator<Rights> iterator = taxonBase.getRights().iterator(); iterator.hasNext();) {\r
+ Rights rights = iterator.next();\r
+ iterator.remove();\r
+ getSession().delete(rights);\r
+ }\r
+ \r
+ if (taxonBase instanceof Taxon){ // is Taxon\r
//taxonRelationships\r
Taxon taxon = (Taxon)taxonBase;\r
- Set<TaxonRelationship> taxRels = taxon.getTaxonRelations();\r
- for (TaxonRelationship taxRel: taxRels){\r
- taxon.removeTaxonRelation(taxRel);\r
- } ;\r
+ \r
+ for (Iterator<TaxonRelationship> iterator = taxon.getRelationsFromThisTaxon().iterator(); iterator.hasNext();){\r
+ TaxonRelationship relationFromThisTaxon = iterator.next();\r
+ iterator.remove();\r
+ \r
+ // decrease children count of taxonomic parent by one\r
+ if (relationFromThisTaxon.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())) {\r
+ Taxon toTaxon = relationFromThisTaxon.getToTaxon(); // parent\r
+ if (toTaxon != null) {\r
+ toTaxon.setTaxonomicChildrenCount(toTaxon.getTaxonomicChildrenCount() - 1); \r
+ }\r
+ }\r
+ relationFromThisTaxon.setToTaxon(null);\r
+ relationFromThisTaxon.setFromTaxon(null);\r
+ getSession().delete(relationFromThisTaxon);\r
+ }\r
+ \r
+ for (Iterator<TaxonRelationship> iterator = taxon.getRelationsToThisTaxon().iterator(); iterator.hasNext();){\r
+ TaxonRelationship relationToThisTaxon = iterator.next();\r
+ iterator.remove();\r
+ \r
+ // set parent cache of child to null\r
+ if (relationToThisTaxon.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())) {\r
+ Taxon fromTaxon = relationToThisTaxon.getFromTaxon(); // child\r
+ if (fromTaxon != null) {\r
+ fromTaxon.nullifyTaxonomicParent();\r
+ }\r
+ }\r
+ relationToThisTaxon.setFromTaxon(null);\r
+ relationToThisTaxon.setToTaxon(null);\r
+ getSession().delete(relationToThisTaxon);\r
+ }\r
+ \r
//SynonymRelationships\r
- Set<SynonymRelationship> synRels = taxon.getSynonymRelations();\r
- for (SynonymRelationship synRel: synRels){\r
- taxon.removeSynonymRelation(synRel);\r
- } ;\r
- }//is Synonym\r
- else if (taxonBase instanceof Synonym){\r
+ for (Iterator<SynonymRelationship> iterator = taxon.getSynonymRelations().iterator(); iterator.hasNext();){\r
+ SynonymRelationship synonymRelation = iterator.next();\r
+ iterator.remove();\r
+ synonymRelation.setAcceptedTaxon(null);\r
+ synonymRelation.setSynonym(null);\r
+ getSession().delete(synonymRelation);\r
+ } \r
+ \r
+ // Descriptions\r
+ for (Iterator<TaxonDescription> iterDesc = taxon.getDescriptions().iterator(); iterDesc.hasNext();) {\r
+ TaxonDescription taxonDescription = iterDesc.next();\r
+ iterDesc.remove();\r
+ //taxonDescription.setTaxon(null);\r
+ Field field = ReflectionUtils.findField(TaxonDescription.class, "taxon", Taxon.class);\r
+ ReflectionUtils.makeAccessible(field);\r
+ ReflectionUtils.setField(field, taxonDescription, null);\r
+ for (Iterator<DescriptionElementBase> iterDescElem = \r
+ taxonDescription.getElements().iterator(); iterDescElem.hasNext();) {\r
+ DescriptionElementBase descriptionElement = iterDescElem.next();\r
+ iterDescElem.remove();\r
+ getSession().delete(descriptionElement);\r
+ }\r
+ getSession().delete(taxonDescription);\r
+ }\r
+ \r
+ taxon.nullifyTaxonomicParent();\r
+\r
+ } else { //is Synonym\r
Synonym synonym = (Synonym)taxonBase;\r
- Set<SynonymRelationship> synRels = synonym.getSynonymRelations();\r
- for (SynonymRelationship synRel: synRels){\r
- synonym.removeSynonymRelation(synRel);\r
+ for (Iterator<SynonymRelationship> iterator = synonym.getSynonymRelations().iterator(); iterator.hasNext();){\r
+ SynonymRelationship synonymRelation = iterator.next();\r
+ iterator.remove();\r
+ synonymRelation.setAcceptedTaxon(null);\r
+ synonymRelation.setSynonym(null);\r
} ;\r
}\r
return super.delete(taxonBase);\r
\r
\r
// TODO add generic return type !!\r
- public List findByName(String queryString, ITitledDao.MATCH_MODE matchMode, int page, int pagesize, boolean onlyAcccepted) {\r
+ public List findByName(String queryString, MatchMode matchMode, int page, int pagesize, boolean onlyAcccepted) {\r
ArrayList<Criterion> criteria = new ArrayList<Criterion>();\r
//TODO ... Restrictions.eq(propertyName, value)\r
return super.findByTitle(queryString, matchMode, page, pagesize, criteria);\r
\r
}\r
\r
- public int countMatchesByName(String queryString, ITitledDao.MATCH_MODE matchMode, boolean onlyAcccepted) {\r
-\r
+ public int countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.countMatchesByName(String queryString, ITitledDao.MATCH_MODE matchMode, boolean onlyAcccepted)");\r
Criteria crit = getSession().createCriteria(type);\r
- crit.add(Restrictions.ilike("persistentTitleCache", matchMode.queryStringFrom(queryString)));\r
+ crit.add(Restrictions.ilike("titleCache", matchMode.queryStringFrom(queryString)));\r
crit.setProjection(Projections.rowCount());\r
int result = ((Integer)crit.list().get(0)).intValue();\r
return result;\r
}\r
\r
\r
- public int countMatchesByName(String queryString, ITitledDao.MATCH_MODE matchMode, boolean onlyAcccepted, List<Criterion> criteria) {\r
-\r
+ public int countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted, List<Criterion> criteria) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.countMatchesByName(String queryString, ITitledDao.MATCH_MODE matchMode, boolean onlyAcccepted, List<Criterion> criteria)");\r
Criteria crit = getSession().createCriteria(type);\r
- crit.add(Restrictions.ilike("persistentTitleCache", matchMode.queryStringFrom(queryString)));\r
+ crit.add(Restrictions.ilike("titleCache", matchMode.queryStringFrom(queryString)));\r
if(criteria != null){\r
for (Criterion criterion : criteria) {\r
crit.add(criterion);\r
return result;\r
}\r
\r
- public int countRelatedTaxa(Taxon taxon, TaxonRelationshipType type) {\r
- Query query = null;\r
+ public int countTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Direction direction) {\r
+ AuditEvent auditEvent = getAuditEventFromContext();\r
+ if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {\r
+ Query query = null;\r
+ \r
+ if(type == null) {\r
+ query = getSession().createQuery("select count(taxonRelationship) from TaxonRelationship taxonRelationship where taxonRelationship."+direction+" = :relatedTaxon");\r
+ } else {\r
+ query = getSession().createQuery("select count(taxonRelationship) from TaxonRelationship taxonRelationship where taxonRelationship."+direction+" = :relatedTaxon and taxonRelationship.type = :type");\r
+ query.setParameter("type",type);\r
+ }\r
+ query.setParameter("relatedTaxon", taxon);\r
\r
- if(type == null) {\r
- query = getSession().createQuery("select count(taxonRelationship) from TaxonRelationship taxonRelationship where taxonRelationship.relatedTo = :relatedTo");\r
+ return ((Long)query.uniqueResult()).intValue();\r
} else {\r
- query = getSession().createQuery("select count(taxonRelationship) from TaxonRelationship taxonRelationship where taxonRelationship.relatedTo = :relatedTo and taxonRelationship.type = :type");\r
- query.setParameter("type",type);\r
+ AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(TaxonRelationship.class,auditEvent.getRevisionNumber());\r
+ query.add(AuditEntity.relatedId(direction.toString()).eq(taxon.getId()));\r
+ query.addProjection(AuditEntity.id().count("id"));\r
+ \r
+ if(type != null) {\r
+ query.add(AuditEntity.relatedId("type").eq(type.getId()));\r
+ }\r
+ \r
+ return ((Long)query.getSingleResult()).intValue();\r
}\r
- \r
- query.setParameter("relatedTo", taxon);\r
- \r
- return ((Long)query.uniqueResult()).intValue();\r
}\r
\r
public int countSynonyms(Taxon taxon, SynonymRelationshipType type) {\r
- Query query = null;\r
- \r
- if(type == null) {\r
- query = getSession().createQuery("select count(synonymRelationship) from SynonymRelationship synonymRelationship where synonymRelationship.relatedTo = :relatedTo");\r
+ AuditEvent auditEvent = getAuditEventFromContext();\r
+ if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {\r
+ Query query = null;\r
+\r
+ if(type == null) {\r
+ query = getSession().createQuery("select count(synonymRelationship) from SynonymRelationship synonymRelationship where synonymRelationship.relatedTo = :relatedTo");\r
+ } else {\r
+ query = getSession().createQuery("select count(synonymRelationship) from SynonymRelationship synonymRelationship where synonymRelationship.relatedTo = :relatedTo and synonymRelationship.type = :type");\r
+ query.setParameter("type",type);\r
+ }\r
+\r
+ query.setParameter("relatedTo", taxon);\r
+\r
+ return ((Long)query.uniqueResult()).intValue();\r
} else {\r
- query = getSession().createQuery("select count(synonymRelationship) from SynonymRelationship synonymRelationship where synonymRelationship.relatedTo = :relatedTo and synonymRelationship.type = :type");\r
- query.setParameter("type",type);\r
+ AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(SynonymRelationship.class,auditEvent.getRevisionNumber());\r
+ query.add(AuditEntity.relatedId("relatedTo").eq(taxon.getId()));\r
+ query.addProjection(AuditEntity.id().count("id"));\r
+ \r
+ if(type != null) {\r
+ query.add(AuditEntity.relatedId("type").eq(type.getId()));\r
+ }\r
+ \r
+ return ((Long)query.getSingleResult()).intValue();\r
}\r
- \r
- query.setParameter("relatedTo", taxon);\r
- \r
- return ((Long)query.uniqueResult()).intValue();\r
}\r
\r
- public int countTaxa(String queryString, Boolean accepted) {\r
- QueryParser queryParser = new QueryParser("name.persistentTitleCache", new SimpleAnalyzer());\r
+ public int count(Class<? extends TaxonBase> clazz, String queryString) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.count(String queryString, Boolean accepted)");\r
+ QueryParser queryParser = new QueryParser(defaultField, new SimpleAnalyzer());\r
\r
try {\r
org.apache.lucene.search.Query query = queryParser.parse(queryString);\r
\r
- FullTextSession fullTextSession = Search.createFullTextSession(this.getSession());\r
+ FullTextSession fullTextSession = Search.getFullTextSession(this.getSession());\r
org.hibernate.search.FullTextQuery fullTextQuery = null;\r
\r
- if(accepted == null) {\r
- fullTextQuery = fullTextSession.createFullTextQuery(query, TaxonBase.class);\r
+ if(clazz == null) {\r
+ fullTextQuery = fullTextSession.createFullTextQuery(query, type);\r
} else {\r
- if(accepted) {\r
- fullTextQuery = fullTextSession.createFullTextQuery(query, Taxon.class);\r
- } else {\r
- fullTextQuery = fullTextSession.createFullTextQuery(query, Synonym.class);\r
- }\r
+ fullTextQuery = fullTextSession.createFullTextQuery(query, clazz);\r
}\r
\r
Integer result = fullTextQuery.getResultSize();\r
}\r
}\r
\r
- public int countTaxaByName(String queryString, Boolean accepted, ReferenceBase sec) {\r
- \r
- Criteria criteria = null;\r
- \r
- if (accepted == true) {\r
- criteria = getSession().createCriteria(Taxon.class);\r
- } else {\r
- criteria = getSession().createCriteria(Synonym.class);\r
- }\r
- \r
- criteria.setFetchMode( "name", FetchMode.JOIN );\r
- criteria.createAlias("name", "name");\r
-\r
- if (sec != null){\r
- if(sec.getId() == 0){\r
- getSession().save(sec);\r
- }\r
- criteria.add(Restrictions.eq("sec", sec ) );\r
- }\r
- if (queryString != null) {\r
- criteria.add(Restrictions.ilike("name.nameCache", queryString));\r
- }\r
- criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));\r
- \r
- return (Integer)criteria.uniqueResult();\r
- }\r
-\r
- public int countTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank) {\r
+// public int countTaxaByName(String queryString, Boolean accepted, ReferenceBase sec) {\r
+// \r
+// SelectMode selectMode = (accepted ? SelectMode.TAXA : SelectMode.SYNONYMS);\r
+// Long count = countTaxaByName(queryString, MatchMode.ANYWHERE, selectMode , sec, null);\r
+// \r
+// return count.intValue();\r
+// }\r
+\r
+ public int countTaxaByName(Class<? extends TaxonBase> clazz, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.countTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank)");\r
Criteria criteria = null;\r
\r
- if(accepted == null) {\r
+ if(clazz == null) {\r
criteria = getSession().createCriteria(TaxonBase.class);\r
} else {\r
- if(accepted) {\r
- criteria = getSession().createCriteria(Taxon.class);\r
- } else {\r
- criteria = getSession().createCriteria(Synonym.class);\r
- }\r
+ criteria = getSession().createCriteria(clazz); \r
}\r
\r
criteria.setFetchMode( "name", FetchMode.JOIN );\r
return (Integer)criteria.uniqueResult();\r
}\r
\r
- public List<TaxonBase> findTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank, Integer pageSize, Integer pageNumber) {\r
+ public List<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank, Integer pageSize, Integer pageNumber) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.findTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank, Integer pageSize, Integer pageNumber)");\r
Criteria criteria = null;\r
\r
- if(accepted == null) {\r
+ if(clazz == null) {\r
criteria = getSession().createCriteria(TaxonBase.class);\r
} else {\r
- if(accepted) {\r
- criteria = getSession().createCriteria(Taxon.class);\r
- } else {\r
- criteria = getSession().createCriteria(Synonym.class);\r
- }\r
+ criteria = getSession().createCriteria(clazz);\r
}\r
\r
criteria.setFetchMode( "name", FetchMode.JOIN );\r
criteria.createAlias("name", "name");\r
\r
- if(genusOrUninomial != null) {\r
+ if(genusOrUninomial == null) {\r
+ criteria.add(Restrictions.isNull("name.genusOrUninomial"));\r
+ } else if(!genusOrUninomial.equals("*")) {\r
criteria.add(Restrictions.eq("name.genusOrUninomial", genusOrUninomial));\r
}\r
\r
- if(infraGenericEpithet != null) {\r
- criteria.add(Restrictions.eq("name.infraGenericEpithet", infraGenericEpithet));\r
- } else {\r
+ if(infraGenericEpithet == null) {\r
criteria.add(Restrictions.isNull("name.infraGenericEpithet"));\r
- }\r
+ } else if(!infraGenericEpithet.equals("*")) {\r
+ criteria.add(Restrictions.eq("name.infraGenericEpithet", infraGenericEpithet));\r
+ } \r
\r
- if(specificEpithet != null) {\r
+ if(specificEpithet == null) {\r
+ criteria.add(Restrictions.isNull("name.specificEpithet"));\r
+ } else if(!specificEpithet.equals("*")) {\r
criteria.add(Restrictions.eq("name.specificEpithet", specificEpithet));\r
+ \r
}\r
\r
- if(infraSpecificEpithet != null) {\r
+ if(infraSpecificEpithet == null) {\r
+ criteria.add(Restrictions.isNull("name.infraSpecificEpithet"));\r
+ } else if(!infraSpecificEpithet.equals("*")) {\r
criteria.add(Restrictions.eq("name.infraSpecificEpithet", infraSpecificEpithet));\r
}\r
\r
return (List<TaxonBase>)criteria.list();\r
}\r
\r
- public List<TaxonRelationship> getRelatedTaxa(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber) {\r
- Query query = null;\r
+ public List<TaxonRelationship> getTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths, Direction direction) {\r
+ AuditEvent auditEvent = getAuditEventFromContext();\r
+ if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {\r
+ Criteria criteria = getSession().createCriteria(TaxonRelationship.class);\r
+ \r
+ criteria.add(Restrictions.eq("relatedTo", taxon));\r
+ if(type != null) {\r
+ criteria.add(Restrictions.eq("type", type));\r
+ } \r
\r
- if(type == null) {\r
- query = getSession().createQuery("select taxonRelationship from TaxonRelationship taxonRelationship join fetch taxonRelationship.relatedFrom where taxonRelationship.relatedTo = :relatedTo");\r
- } else {\r
- query = getSession().createQuery("select taxonRelationship from TaxonRelationship taxonRelationship join fetch taxonRelationship.relatedFrom where taxonRelationship.relatedTo = :relatedTo and taxonRelationship.type = :type");\r
- query.setParameter("type",type);\r
- }\r
+ addOrder(criteria,orderHints);\r
\r
- query.setParameter("relatedTo", taxon);\r
+ if(pageSize != null) {\r
+ criteria.setMaxResults(pageSize);\r
+ if(pageNumber != null) {\r
+ criteria.setFirstResult(pageNumber * pageSize);\r
+ } else {\r
+ criteria.setFirstResult(0);\r
+ }\r
+ }\r
\r
- if(pageSize != null) {\r
- query.setMaxResults(pageSize);\r
- if(pageNumber != null) {\r
- query.setFirstResult(pageNumber * pageSize);\r
- } else {\r
- query.setFirstResult(0);\r
+ List<TaxonRelationship> result = (List<TaxonRelationship>)criteria.list();\r
+ defaultBeanInitializer.initializeAll(result, propertyPaths);\r
+ \r
+ return result;\r
+ } else {\r
+ AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(TaxonRelationship.class,auditEvent.getRevisionNumber());\r
+ query.add(AuditEntity.relatedId("relatedTo").eq(taxon.getId()));\r
+ \r
+ if(type != null) {\r
+ query.add(AuditEntity.relatedId("type").eq(type.getId()));\r
}\r
+ \r
+ if(pageSize != null) {\r
+ query.setMaxResults(pageSize);\r
+ if(pageNumber != null) {\r
+ query.setFirstResult(pageNumber * pageSize);\r
+ } else {\r
+ query.setFirstResult(0);\r
+ }\r
+ }\r
+ \r
+ List<TaxonRelationship> result = (List<TaxonRelationship>)query.getResultList();\r
+ defaultBeanInitializer.initializeAll(result, propertyPaths);\r
+ \r
+ // Ugly, but for now, there is no way to sort on a related entity property in Envers,\r
+ // and we can't live without this functionality in CATE as it screws up the whole \r
+ // taxon tree thing\r
+ if(orderHints != null && !orderHints.isEmpty()) {\r
+ SortedSet<TaxonRelationship> sortedList = new TreeSet<TaxonRelationship>(new TaxonRelationshipFromTaxonComparator());\r
+ sortedList.addAll(result);\r
+ return new ArrayList<TaxonRelationship>(sortedList);\r
+ }\r
+ \r
+ return result;\r
+ }\r
+ }\r
+ \r
+ class TaxonRelationshipFromTaxonComparator implements Comparator<TaxonRelationship> {\r
+\r
+ public int compare(TaxonRelationship o1, TaxonRelationship o2) {\r
+ return o1.getFromTaxon().getTitleCache().compareTo(o2.getFromTaxon().getTitleCache());\r
}\r
\r
- return (List<TaxonRelationship>)query.list();\r
}\r
\r
- public List<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber) {\r
- Query query = null;\r
+ public List<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ AuditEvent auditEvent = getAuditEventFromContext();\r
+ if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {\r
+ Criteria criteria = getSession().createCriteria(SynonymRelationship.class);\r
+ \r
+ criteria.add(Restrictions.eq("relatedTo", taxon));\r
+ if(type != null) {\r
+ criteria.add(Restrictions.eq("type", type));\r
+ } \r
\r
- if(type == null) {\r
- query = getSession().createQuery("select synonymRelationship from SynonymRelationship synonymRelationship join fetch synonymRelationship.relatedFrom where synonymRelationship.relatedTo = :relatedTo");\r
- } else {\r
- query = getSession().createQuery("select synonymRelationship from SynonymRelationship synonymRelationship join fetch synonymRelationship.relatedFrom where synonymRelationship.relatedTo = :relatedTo and synonymRelationship.type = :type");\r
- query.setParameter("type",type);\r
- }\r
+ addOrder(criteria,orderHints);\r
\r
- query.setParameter("relatedTo", taxon);\r
+ if(pageSize != null) {\r
+ criteria.setMaxResults(pageSize);\r
+ if(pageNumber != null) {\r
+ criteria.setFirstResult(pageNumber * pageSize);\r
+ } else {\r
+ criteria.setFirstResult(0);\r
+ }\r
+ }\r
\r
- if(pageSize != null) {\r
- query.setMaxResults(pageSize);\r
- if(pageNumber != null) {\r
- query.setFirstResult(pageNumber * pageSize);\r
- } else {\r
- query.setFirstResult(0);\r
+ List<SynonymRelationship> result = (List<SynonymRelationship>)criteria.list();\r
+ defaultBeanInitializer.initializeAll(result, propertyPaths);\r
+ \r
+ return result;\r
+ } else {\r
+ AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(SynonymRelationship.class,auditEvent.getRevisionNumber());\r
+ query.add(AuditEntity.relatedId("relatedTo").eq(taxon.getId()));\r
+ \r
+ if(type != null) {\r
+ query.add(AuditEntity.relatedId("type").eq(type.getId()));\r
+ }\r
+ \r
+ if(pageSize != null) {\r
+ query.setMaxResults(pageSize);\r
+ if(pageNumber != null) {\r
+ query.setFirstResult(pageNumber * pageSize);\r
+ } else {\r
+ query.setFirstResult(0);\r
+ }\r
}\r
+ \r
+ List<SynonymRelationship> result = (List<SynonymRelationship>)query.getResultList();\r
+ defaultBeanInitializer.initializeAll(result, propertyPaths);\r
+ \r
+ return result;\r
}\r
- \r
- return (List<SynonymRelationship>)query.list();\r
}\r
\r
- public List<TaxonBase> searchTaxa(String queryString, Boolean accepted, Integer pageSize, Integer pageNumber) {\r
- QueryParser queryParser = new QueryParser("name.persistentTitleCache", new SimpleAnalyzer());\r
+ public List<TaxonBase> search(Class<? extends TaxonBase> clazz, String queryString,Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.searchTaxa(String queryString, Boolean accepted, Integer pageSize, Integer pageNumber)");\r
+ QueryParser queryParser = new QueryParser(defaultField, new SimpleAnalyzer());\r
List<TaxonBase> results = new ArrayList<TaxonBase>();\r
\r
try {\r
org.apache.lucene.search.Query query = queryParser.parse(queryString);\r
\r
- FullTextSession fullTextSession = Search.createFullTextSession(getSession());\r
+ FullTextSession fullTextSession = Search.getFullTextSession(getSession());\r
org.hibernate.search.FullTextQuery fullTextQuery = null;\r
- Criteria criteria = null;\r
\r
- if(accepted == null) {\r
+ if(clazz == null) {\r
fullTextQuery = fullTextSession.createFullTextQuery(query, TaxonBase.class);\r
- criteria = getSession().createCriteria( TaxonBase.class );\r
} else {\r
- if(accepted) {\r
- fullTextQuery = fullTextSession.createFullTextQuery(query, Taxon.class);\r
- criteria = getSession().createCriteria( Taxon.class );\r
- } else {\r
- fullTextQuery = fullTextSession.createFullTextQuery(query, Synonym.class);\r
- criteria = getSession().createCriteria( Synonym.class );\r
- }\r
+ fullTextQuery = fullTextSession.createFullTextQuery(query, clazz);\r
}\r
\r
- org.apache.lucene.search.Sort sort = new Sort(new SortField("name.titleCache_forSort"));\r
- fullTextQuery.setSort(sort);\r
+ addOrder(fullTextQuery,orderHints);\r
\r
- criteria.setFetchMode( "name", FetchMode.JOIN );\r
- fullTextQuery.setCriteriaQuery(criteria);\r
- \r
if(pageSize != null) {\r
fullTextQuery.setMaxResults(pageSize);\r
if(pageNumber != null) {\r
}\r
}\r
\r
- return (List<TaxonBase>)fullTextQuery.list();\r
+ List<TaxonBase> result = (List<TaxonBase>)fullTextQuery.list();\r
+ defaultBeanInitializer.initializeAll(result, propertyPaths);\r
+ return result;\r
\r
} catch (ParseException e) {\r
throw new QueryParseException(e, queryString);\r
}\r
\r
public void purgeIndex() {\r
- FullTextSession fullTextSession = Search.createFullTextSession(getSession());\r
- \r
- fullTextSession.purgeAll(type); // remove all taxon base from indexes\r
- // fullTextSession.flushToIndexes() not implemented in 3.0.0.GA\r
+ FullTextSession fullTextSession = Search.getFullTextSession(getSession());\r
+ for(Class clazz : indexedClasses) {\r
+ fullTextSession.purgeAll(clazz); // remove all taxon base from indexes\r
+ }\r
+ fullTextSession.flushToIndexes();\r
}\r
\r
public void rebuildIndex() {\r
- FullTextSession fullTextSession = Search.createFullTextSession(getSession());\r
+ FullTextSession fullTextSession = Search.getFullTextSession(getSession());\r
\r
for(TaxonBase taxonBase : list(null,null)) { // re-index all taxon base\r
Hibernate.initialize(taxonBase.getName());\r
fullTextSession.index(taxonBase);\r
}\r
- // fullTextSession.flushToIndexes() not implemented in 3.0.0.GA\r
+ fullTextSession.flushToIndexes();\r
}\r
\r
public void optimizeIndex() {\r
- FullTextSession fullTextSession = Search.createFullTextSession(getSession());\r
+ FullTextSession fullTextSession = Search.getFullTextSession(getSession());\r
SearchFactory searchFactory = fullTextSession.getSearchFactory();\r
- searchFactory.optimize(type); // optimize the indices ()\r
- // fullTextSession.flushToIndexes() not implemented in 3.0.0.GA\r
+ for(Class clazz : indexedClasses) {\r
+ searchFactory.optimize(clazz); // optimize the indices ()\r
+ }\r
+ fullTextSession.flushToIndexes();\r
}\r
\r
public String suggestQuery(String queryString) {\r
- try {\r
- String alternativeQueryString = null;\r
- alternativeSpellingSuggestionParser.parse(queryString);\r
- org.apache.lucene.search.Query alternativeQuery = alternativeSpellingSuggestionParser.suggest(queryString);\r
- if(alternativeQuery != null) {\r
- alternativeQueryString = alternativeQuery.toString("name.persistentTitleCache");\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.suggestQuery(String queryString)");\r
+ String alternativeQueryString = null;\r
+ if (alternativeSpellingSuggestionParser != null) {\r
+ try {\r
+\r
+ alternativeSpellingSuggestionParser.parse(queryString);\r
+ org.apache.lucene.search.Query alternativeQuery = alternativeSpellingSuggestionParser.suggest(queryString);\r
+ if (alternativeQuery != null) {\r
+ alternativeQueryString = alternativeQuery\r
+ .toString("name.titleCache");\r
+ }\r
+\r
+ } catch (ParseException e) {\r
+ throw new QueryParseException(e, queryString);\r
}\r
- return alternativeQueryString;\r
- } catch (ParseException e) {\r
- throw new QueryParseException(e, queryString);\r
}\r
+ return alternativeQueryString;\r
}\r
-}
\ No newline at end of file
+}\r
BGBM BDI Projects / cdmlib.git / blobdiff